RcppArmadillo : accelerating R with high-performance C++ linear algebra

The R statistical environment and language has demonstrated particular strengths for interactive development of statistical algorithms, as well as data modelling and visualisation. Its current implementation has an interpreter at its core which may result in a performance penalty in comparison to directly executing user algorithms in the native machine code of the host CPU. In contrast, the C++ language has no built-in visualisation capabilities, handling of linear algebra or even basic statistical algorithms; however, user programs are converted to high-performance machine code, ahead of execution. A new method avoids possible speed penalties in R by using the Rcpp extension package in conjunction with the Armadillo C++ matrix library. In addition to the inherent performance advantages of compiled code, Armadillo provides an easy-to-use template-based meta-programming framework, allowing the automatic pooling of several linear algebra operations into one, which in turn can lead to further speedups. With the aid of Rcpp and Armadillo, conversion of linear algebra centered algorithms from R to C++ becomes straightforward. The algorithms retains the overall structure as well as readability, all while maintaining a bidirectional link with the host R environment. Empirical timing comparisons of R and C++ implementations of a Kalman filtering algorithm indicate a speedup of several orders of magnitude.

Nutrient removal from wastewaters using high performance materials

Return side streams from anaerobic digesters and dewatering facilities at wastewater treatment plants (WWTPs) contribute a significant proportion of the total nitrogen load on a mainstream process. Similarly, significant phosphate loads are also recirculated in biological nutrient removal (BNR) wastewater treatment plants. Ion exchange using a new material, known by the name MesoLite, shows strong potential for the removal of ammonia from these side streams and an opportunity to concurrently reduce phosphate levels. A pilot plant was designed and operated for several months on an ammonia rich centrate from a dewatering centrifuge at the Oxley Creek WWTP, Brisbane, Australia. The system operated with a detention time in the order of one hour and was operated for between 12 and 24 hours prior to regeneration with a sodium rich solution. The same pilot plant was used to demonstrate removal of phosphate from an abattoir wastewater stream at similar flow rates. Using MesoLite materials, >90% reduction of ammonia was achieved in the centrate side stream. A full-scale process would reduce the total nitrogen load at the Oxley Creek WWTP by at least 18%. This reduction in nitrogen load consequently improves the TKN/COD ratio of the influent and enhances the nitrogen removal performance of the biological nutrient removal process.

Pharmacokinetics of cimifugin in rat plasma after oral administration of the extract of Saposhnikovia divaricatae root : Determination of cimifugin by high performance liquid chromatography coupled with solid phase extraction

High performance liquid chromatography (HPLC) coupled with the solid phase extraction method was developed for determining cimifugin (a coumarin derivative; one of Saposhnikovia divaricatae's constituents) in rat plasma after oral administration of Saposhnikovia divaricatae extract (SDE), and the pharmacokinetics of cimifugin either in SDE or as a single compound was investigated. The HPLC analysis was performed on a commercially available column (4.6 mm x 200 mm, 5 pm) with the isocratic elution of solvent A (Methanol) and solvent B (Water) (A:B=60:40) and the detection wavelength was set at 250 nm. The calibration curve was linear over the range of 0.100-10.040 microg/mL. The limit of detection was 30 ng/mL. At the rat plasma concentrations of 0.402, 4.016, 10.040 microg/mL, the intra-day precision was 6.21%, 3.98%, and 2.23%; the inter-day precision was 7.59%, 4.26%, and 2.09%, respectively. The absolute recovery was 76.58%, 76.61%, and 77.67%, respectively. When the dosage of SDE was equal to the pure compound calculated by the amount of cimifugin, it was found to have two maximum peaks while the pure compound only showed one peak in the plasma concentration-time curve. The pharmacokinetic characteristics of SDE showed the superiority of the extract and the properties of traditional Chinese medicine.

Simultaneous determination of aldrin, dieldrin, endrin, heptachlor, and p,p'-DDT in medicinal plant extracts using a novel high performance liquid chromatography method

A high performance liquid chromatographic method for the simultaneous determination of five organochlorine pesticides (aldrin, p,p’-DDT, dieldrin, endrin, and heptachlor) was developed. The method was used to determine the levels of these pesticides in medicinal plant samples. Analysis was carried out using a Merck LiChrospher 100 RP C18 (5 μm) column with a gradient solvent system of acetonitrile-water and PDA UV detection (224 nm). Quantification was carried out by the external standard method. The limit of detection for the utilized method was below the local legal limits (ANZFA) for similar plant materials for all 5 pesticides excepting endrin. Medicinal plant extracts were further analyzed by conventional GC-ECD and GC-NPD means using SPE and GPC cleanup as required.

High performance liquid chromatography determined alkamide levels in Australian-grown Echinacea spp.

Extracts of Echinacea spp. are widely used as therapeutic immunostimulants with such activity being attributed in part to the alkamide fractions of these plants. Using high performance liquid chromatography, the levels of 8 alkamides, including 2 tetraene alkamides (dodeca-2E, 4E, 8Z, 10E/Z-tetraenoic acid isobutylamide), were quantitatively determined in 2 Australian-grown Echinacea spp. Overall, the levels of alkamides in Australian-grown E. angustifolia were found to be comparable with levels obtained in this study and other studies for USA and European Echinacea spp. However, results obtained for one sample of E. angustifolia suggested that it may have been mislabelled and that it was most likely a sample of E. pallida. Levels of tetraene alkamides in Australian-grown E. purpurea were also similar to, if not higher, than levels which have been reported for the same species grown in Germany and the USA. Preliminary studies on the stability of alkamide compounds in E. angustifolia indicated that they are susceptible to degradation, with a 13% loss of alkamide level over 2 months. Overall, results indicate that there is considerable potential to develop Echinacea as a viable crop in Australia.

A high performance feedback active noise control system

In many active noise control (ANC) applications, an online secondary path modelling method that uses a white noise as a training signal is required. This paper proposes a new feedback ANC system. Here we modified both the FxLMS and the VSS-LMS algorithms to raised noise attenuation and modelling accuracy for the overall system. The proposed algorithm stops injection of the white noise at the optimum point and reactivate the injection during the operation, if needed, to maintain performance of the system. Preventing continuous injection of the white noise increases the performance of the proposed method significantly and makes it more desirable for practical ANC systems. Computer simulation results shown in this paper indicate effectiveness of the proposed method.

High performance electrochromic devices based on anodized nanoporous Nb2O5

Despite the predictions, the true potential of Nb2O5 for electrochromic applications has yet to be fully realized. In this work, three-dimensional (3D) compact and well-ordered nanoporous Nb2O5 films are synthesized by the electrochemical anodization of niobium thin films. These films are formed using RF sputtering and then anodized in an electrolyte containing ethylene glycol, ammonium fluoride, and small water content (4%) at 50 °C which resulted in low embedded impurities within the structure. Characterization of the anodized films shows that a highly crystalline orthorhombic phase of Nb2O5 is obtained after annealing at 450 °C. The 3D structure provides a template consisting of a large concentration of active sites for ion intercalation, while also ensuring low scattering directional paths for electrons. These features enhance the coloration efficiency to 47.0 cm2 C?1 (at 550 nm) for a 500 nm thick film upon Li+ ion intercalation. Additionally, the Nb2O5 electrochromic device shows a high bleached state transparency and large optical modulation.

Characteristics of high-performance ambipolar organic field-effect transistors based on a diketopyrrolopyrrole-benzothiadiazole copolymer

In this paper, we report the device characteristics of ambipolar thin-film transistors (TFTs) based on a diketopyrrolopyrrole-benzothiadiazole copolymer. This polymer semiconductor exhibits the largest comparable electron and hole mobility values in a single organic semiconductor. The key to realizing such high mobility values, which are $0.5&cm}{2}/\hbox{V}̇\hbox{s, is molecular design, i.e., the use of suitable surface treatments of the source/drain contact electrodes and device architectures, particularly top-gate configurations. The subthreshold characteristics of the TFT devices are greatly improved by the use of dual-gate device geometry. We also report the first measurement of the velocity distribution of electron and hole velocities in an ambipolar organic semiconductor.

Design and modification of three-component randomly incorporated copolymers for high performance organic photovoltaic applications

In this study we report the molecular design, synthesis, characterization, and photovoltaic properties of a series of diketopyrrolopyrrole (DPP) and dithienothiophene (DTT) based donor-acceptor random copolymers. The six random copolymers are obtained via Stille coupling polymerization using various concentration ratios of donor to acceptor in the conjugated backbone. Bis(trimethylstannyl)thiophene was used as the bridge block to link randomly with the two comonomers 5-(bromothien-2-yl)-2,5-dialkylpyrrolo[3,4-c]pyrrole-1, 4-dione and 2,6-dibromo-3,5-dipentadecyl-dithieno[3,2-b;2′,3′-d] thiophene. The optical properties of these copolymers clearly reveal a change in the absorption band through optimization of the donor-acceptor ratio in the backbone. Additionally, the solution processability of the copolymers is modified through the attachment of different bulky alkyl chains to the lactam N-atoms of the DPP moiety. Applications of the polymers as light-harvesting and electron-donating materials in solar cells, in conjunction with PCBM as acceptor, show power conversion efficiencies (PCEs) of up to 5.02%.

Poly(2,5-bis(2-octyldodecyl)-3,6-di(furan-2-yl)-2,5-dihydro-pyrrolo[3,4-c] pyrrole-1,4-dione-co-thieno[3,2-b]thiophene): A high performance polymer semiconductor for both organic thin film transistors and organic photovoltaics

A new diketopyrrolopyrrole (DPP)-containing donor-acceptor polymer, poly(2,5-bis(2-octyldodecyl)-3,6-di(furan-2-yl)-2,5-dihydro-pyrrolo[3,4-c] pyrrole-1,4-dione-co-thieno[3,2-b]thiophene) (PDBF-co-TT), is synthesized and studied as a semiconductor in organic thin film transistors (OTFTs) and organic photovoltaics (OPVs). High hole mobility of up to 0.53 cm 2 V -1 s -1 in bottom-gate, top-contact OTFT devices is achieved owing to the ordered polymer chain packing and favoured chain orientation, strong intermolecular interactions, as well as uniform film morphology of PDBF-co-TT. The optimum band gap of 1.39 eV and high hole mobility make this polymer a promising donor semiconductor for the solar cell application. When paired with a fullerene acceptor, PC 71BM, the resulting OPV devices show a high power conversion efficiency of up to 4.38% under simulated standard AM1.5 solar illumination.

Collection and determination of nucleotide metabolites in neonatal and adult saliva by high performance liquid chromatography with tandem mass spectrometry

Saliva contains a number of biochemical components which may be useful for diagnosis/monitoring of metabolic disorders, and as markers of cancer or heart disease. Saliva collection is attractive as a non-invasive sampling method for infants and elderly patients. We present a method suitable for saliva collection from neonates. We have applied this technique for the determination of salivary nucleotide metabolites. Saliva was collected from 10 healthy neonates using washed cotton swabs, and directly from 10 adults. Two methods for saliva extraction from oral swabs were evaluated. The analytes were then separated using high performance liquid chromatography (HPLC) with tandem mass spectrometry (MS/MS). The limits of detection for 14 purine/pyrimidine metabolites were variable, ranging from 0.01 to 1.0 mu M. Recovery of hydrophobic purine/pyrimidine metabolites from cotton tips was consistently high using water/acetonitrile extraction (92.7-111%) compared with water extraction alone. The concentrations of these metabolites were significantly higher in neonatal saliva than in adults. Preliminary ranges for nucleotide metabolites in neonatal and adult saliva are reported. Hypoxanthine and xanthine were grossly raised in neonates (49.3 +/- 25.4; 30.9 +/- 19.5 mu M respectively) compared to adults (4.3 +/- 3.3; 4.6 +/- 4.5 mu M); nucleosides were also markedly raised in neonates. This study focuses on three essential details: contamination of oral swabs during manufacturing and how to overcome this; weighing swabs to accurately measure small saliva volumes; and methods for extracting saliva metabolites of interest from cotton swabs. A method is described for determining nucleotide metabolites using HPLC with photo-diode array or MS/MS. The advantages of utilising saliva are highlighted. Nucleotide metabolites were not simply in equilibrium with plasma, but may be actively secreted into saliva, and this process is more active in neonates than adults. (C) 2013 Elsevier B.V. All rights reserved.

High performance all-carbon thin film supercapacitors

We fabricated high performance supercapacitors by using all carbon electrodes, with volume energy in the order of 10−3 Whcm−3, comparable to Li-ion batteries, and power densities in the range of 10 Wcm−3, better than laser-scribed-graphene supercapacitors. All-carbon supercapacitor electrodes are made by solution processing and filtering electrochemically-exfoliated graphene sheets mixed with clusters of spontaneously entangled multiwall carbon nanotubes. We maximize the capacitance by using a 1:1 weight ratio of graphene to multi-wall carbon nanotubes and by controlling their packing in the electrode film so as to maximize accessible surface and further enhance the charge collection. This electrode is transferred onto a plastic-paper-supported double-wall carbon nanotube film used as current collector. These all-carbon thin films are combined with plastic paper and gelled electrolyte to produce solid-state bendable thin film supercapacitors. We assembled supercapacitor cells in series in a planar configuration to increase the operating voltage and find that the shape of our supercapacitor film strongly affects its capacitance. An in-line superposition of rectangular sheets is superior to a cross superposition in maintaining high capacitance when subject to fast charge/discharge cycles. The effect is explained by addressing the mechanism of ion diffusion into stacked graphene sheets.